dot plot and html file

[xucaoling]

Dear liumz,
Thank you very much for your scripts, when i use define_statistics_add_filter.py, it shows:

#Plot dot plot
cmd = "/home/mengzhu/Scripts/R/TranslocPlot.R results/{}_Editing_events.tab results/{}_Editing_events_dot_plot.pdf \
       binsize=2000000 assembly={} plotshape=octogon strand=0".format(basename,basename,genome)
print(cmd)
os.system(cmd)

#generate html file
cmd = "/home/mengzhu/github/PEM-Q/tools/R/TranslocHTMLReads_PEMQ.pl results/{}_Editing_events.tab results/{}_Editing_events.html \
       --primer {} -adapter {}".format(basename,basename,primer,adapter)
print(cmd)
os.system(cmd)

But i do not find TranslocPlot.R and TranslocHTMLReads_PEMQ.pl and DSB_filter_update.py, Could you share it?

[liumz93]

Hi xucaoling, I'll get these disappearing files fixed soon, please try git clone and run again then.

[liumz93]

fixed already.

[kclem]

Thanks @liumz93

The script 'TranslocPlot.R' calls

  source_local("Rsub.R")
  source_local("TranslocHelper.R")

Do you have those files as well?

[liumz93]

Sorry for the problems, I have provided explanatory notes in README.md, Thanks!

[YanpingHu]

Dear liumz,
Thank you very much for your scripts, when i use define_statistics_add_filter.py, it shows:

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
close_inver.drop(columns=['Microhomolog_len'], inplace=True)
Error in file(file, "rt") :
Calls: getCytoBands -> read.delim -> read.table -> file
Warning message:
In file(file, "rt") :
can't open '/D1/DB/Genome/Human/bwa_indexes/GRCh38/annotation/cytoBand.txt': There is no file or directory for that
Stop execution
Can't locate PerlSub.pl in @inc (@inc contains: /D1/Bio/CRISPR/PemSeq/lib /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /D1/APP/Script/Anaconda/lib/site_perl/5.34.0/x86_64-linux-thread-multi /D1/APP/Script/Anaconda/lib/site_perl/5.34.0 /D1/APP/Script/Anaconda/lib/5.34.0/x86_64-linux-thread-multi /D1/APP/Script/Anaconda/lib/5.34.0 .) at /D1/Bio/CRISPR/PemSeq/tools/TranslocHTMLReads_PEMQ.pl line 21.

But i do not find cytoBand.txt, refGene.bed and PerlSub.pl, Could you share it?

[liumz93]

Hi YanpinHu,

Now you can find the PerlSub.pl in the tool folder. As for cytoBand.txt, refGene.bed, you can download them from UCSC genome browser. For hg38: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/

Thanks,

[YanpingHu]

Thanks! The code is running properly.